title: An alternative pathway for Alu retrotransposition suggests a role in DNA double-strand break repair.
abstract: The Alu family is a highly successful group of non-LTR retrotransposons ubiquitously found in primate genomes. Similar to the L1 retrotransposon family, Alu elements integrate primarily through an endonuclease-dependent mechanism termed target site-primed reverse transcription (TPRT). Recent studies have suggested that, in addition to TPRT, L1 elements occasionally utilize an alternative endonuclease-independent pathway for genomic integration. To determine whether an analogous mechanism exists for Alu elements, we have analyzed three publicly available primate genomes (human, chimpanzee and rhesus macaque) for endonuclease-independent recently integrated or lineage specific Alu insertions. We recovered twenty-three examples of such insertions and show that these insertions are recognizably different from classical TPRT-mediated Alu element integration. We suggest a role for this process in DNA double-strand break repair and present evidence to suggest its association with intra-chromosomal translocations, in-vitro RNA recombination (IVRR), and synthesis-dependent strand annealing (SDSA).
authors.affiliation: Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA 70803, USA.
authors.forename: Deepa
authors.initials: D
authors.lastname: Srikanta
authors.forename: Shurjo K
authors.initials: SK
authors.lastname: Sen
authors.forename: Charles T
authors.initials: CT
authors.lastname: Huang
authors.forename: Erin M
authors.initials: EM
authors.lastname: Conlin
authors.forename: Ryan M
authors.initials: RM
authors.lastname: Rhodes
authors.forename: Mark A
authors.initials: MA
authors.lastname: Batzer
mesh_terms: D020087:Alu Elements / Q000235:genetics*; D000818:Animals; D019295:Computational Biology; D053903:DNA Breaks, Double-Stranded; D004260:DNA Repair; D015894:Genome, Human; D006801:Humans; D008253:Macaca mulatta; D008969:Molecular Sequence Data; D002679:Pan troglodytes; D018626:Retroelements / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid
chemical_list: D018626:Retroelements